Pairing beyond the Seed Supports MicroRNA Targeting Specificity

Mol Cell. 2016 Oct 20;64(2):320-333. doi: 10.1016/j.molcel.2016.09.004. Epub 2016 Oct 6.


To identify endogenous miRNA-target sites, we isolated AGO-bound RNAs from Caenorhabditis elegans by individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP), which fortuitously also produced miRNA-target chimeric reads. Through the analysis of thousands of reproducible chimeras, pairing to the miRNA seed emerged as the predominant motif associated with functional interactions. Unexpectedly, we discovered that additional pairing to 3' sequences is prevalent in the majority of target sites and leads to specific targeting by members of miRNA families. By editing an endogenous target site, we demonstrate that 3' pairing determines targeting by specific miRNA family members and that seed pairing is not always sufficient for functional target interactions. Finally, we present a simplified method, chimera PCR (ChimP), for the detection of specific miRNA-target interactions. Overall, our analysis revealed that sequences in the 5' as well as the 3' regions of a miRNA provide the information necessary for stable and specific miRNA-target interactions in vivo.

Keywords: ALG-1; C. elegans; chimeras; iCLIP; miRNA family; microRNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Base Pairing
  • Base Sequence
  • Binding Sites
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans / metabolism
  • Caenorhabditis elegans Proteins / genetics*
  • Caenorhabditis elegans Proteins / metabolism
  • Exons
  • Gene Expression Regulation
  • Immunoprecipitation / methods
  • Introns
  • MicroRNAs / classification
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Protein Binding
  • RNA, Helminth / genetics*
  • RNA, Helminth / metabolism
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • RNA, Small Nucleolar / genetics
  • RNA, Small Nucleolar / metabolism
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism


  • ALG-1 protein, C elegans
  • Caenorhabditis elegans Proteins
  • MicroRNAs
  • RNA, Helminth
  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA, Small Nucleolar
  • RNA-Binding Proteins